## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

TES dynamics

Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.6)... Done.
## Bootstrap (r = 0.68)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Cut the tree at an optimal number of clusters

Clustering statistics: Cluster number: 5

## [1] "ORF10, ORF11"                 "ORF27, ORF26, ORF25"         
## [3] "ORF37, ORF36, ORF35, ORF35.5" "ORF41, ORF42, OF43"          
## [5] "ORF64_1"                      "ORF24"
## [1] 6

Clustering statistics: Cluster number: 6

## [1] "ORF10, ORF11"                 "ORF27, ORF26, ORF25"         
## [3] "ORF37, ORF36, ORF35, ORF35.5" "ORF41, ORF42, OF43"          
## [5] "ORF24"                        "ORF64_1"
## [1] 6

Clustering statistics: Cluster number: 7

## [1] "ORF10, ORF11"                 "ORF27, ORF26, ORF25"         
## [3] "ORF37, ORF36, ORF35, ORF35.5" "ORF41, ORF42, OF43"          
## [5] "ORF24"                        "ORF64_1"
## [1] 6

Selected number of clusters: 6

## [1] "ORF10, ORF11"                 "ORF27, ORF26, ORF25"         
## [3] "ORF37, ORF36, ORF35, ORF35.5" "ORF41, ORF42, OF43"          
## [5] "ORF24"                        "ORF64_1"
## [1] 6

Remove genes from clusters ?

## The following genes were removed from their corresponding clusters 
##            as their silhouette widths were lower than 0.1 and their distance from the group centroid was higher than 0.5: 
## ORF10, ORF11
## ORF27, ORF26, ORF25
## ORF37, ORF36, ORF35, ORF35.5
## ORF41, ORF42, OF43
## ORF24
## ORF64_1

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

Combined Kinetic classes

De Novo Clusters

Literature clusters